According to JPA specification we can define multiple "persistence-unit" elements (i.e. like below) in persistence.xml file and can easily refer them inside Dao layers as this. public class PolarDaoImpl { @PersistenceContext(unitName="PolarPU") protected EntityManager entityManager; -- } public class BearDaoImpl { @PersistenceContext(unitName="BearPU") protected EntityManager entityManager; -- } Checkout sample persistence.xml <?xml version="1.0" encoding="UTF-8"?> <persistence version="2.0" xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"> <!-- Database 1 --> <persistence-unit name="PolarPU" transaction-type="RESOURCE_LOCAL"> ...